Whatever you did to get 1 million points a day on your site.. I want in.. the name of your marketer please!
I agree with condensing this into a heatmap or a set of RRDs.. one for X.. one for Y.. one for x * (y * max_height)). You can easily query RRDs later on.. even multiple RRD files at once.
Also.. don't be afraid of flat files. They compress well.